Protein-Ligand Complex Water Stripping Inquiry

User discussions
1

GROMACS version: 2022.1
GROMACS modification: Yes/No
Here post your question:

Hello towards the above topic, my docked complex exhibits strategically placed waters via a docking platform, accordingly is there a way around not stripping out these pivotal waters when working through the Protein-Ligand Complex Tutorial i.e. maybe another software?

Thanks:)

2

pdb2gmx can handle water molecules but it will not write constraints to the topology as normal. You’ll have to edit the topology manually by hand to use SETTLE if you want to.

3

Hi Justin thank you for your kind update:).

When I executed the pdb2gmx command I selected a variety of forcefields and water models
which all resulted in the below error:

Fatal error:
Residue ‘H2O’ not found in residue topology database

Accordingly I only generated a blank topol.top file.

With you now knowing this please let me know if you would still your former answer?
(I could not find this answer in the forum nor error website.)

Thanks:)

4

You can find and solution to that error at the Errors page. It’s one of the most frequently asked questions and one I’ve answered probably hundreds of times.

5

Hello Justin thank you for your kind update:).

…and yes I had read this page and its associated rtp page, however, I did not see
the SETTLE that you recommended within this, ill search for just SETTLE and or
just follow these pages I had read, thanks:)